I think perhaps one difference between Al Qaeda and ISIS (correct me if I'm wrong about this) is that Al Qaeda views themselves as upholding morality and therefore being on the side of good, even if they're "unpopular". (As do many terrorists - Al Qaeda is not unique in this regard, nor should we be sympathetic towards them)
ISIS, on the other hand, seems more interested in basically subjugating everyone. They're less terrorists, and more wannabe tyrants.